Official git repository for Biopython (originally converted from CVS)
- python
- bioinformatics
- genomics
- biopython
Repository Index
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Official repository for the Boltz biomolecular interaction models
- binding-prediction
- drug-discovery
- protein-structure
Deep probabilistic analysis of single-cell and spatial omics data
- scrna-seq
- variational-bayes
- variational-autoencoder
- cite-seq
ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.
A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)
- drug-repurposing
- deep-learning
- drug-target-interactions
- toolkit
🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free.
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena
- foundation-models
- genomics
- language-models
C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
- variant-calling
- genomics
- vcf-manipulation
- genotyping
Fast, sensitive and accurate integration of single-cell data with Harmony
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
- sequence-alignment
- edit-distance
- levehnstein-distance
- library
Generative biopolymer design with rich conditioning.
[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome
- dataset
- dna
- dna-processing
- dna-training
RNA Velocity generalized through dynamical modeling
Official repository for the ProteinGym benchmarks
- benchmark
- computational-biology
- protein
- protein-design
A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
- bioinformatics
- taxonomy
- cross-platform
- lineage
Sequential regulatory activity predictions with deep convolutional neural networks.
A dependency-free cross-platform swiss army knife for PDB files.
- python
- protein
- pdb
- bioinformatics
Native R and Python sample-deletion robustness for omics: candidate certificates, minimum deletion bounds, Bioconductor model refits and donor-level pseudobulk
- bioinformatics
- exact-optimization
- metabolomics
- paired-data
RNA-seq prediction with deep convolutional neural networks.
Schema and generated objects for biolink data model and upper ontology
- biolink
- monarchinitiative
- gene-ontology
- datamodel
talk with NCBI entrez using R